Researchers writing in the journal Thorax found that eating apples weekly could reduce childhood asthma, while oily fish could cut eczema.
The researchers added that such a study could help influence public intervention policy in the future.
This study adds further credence to the potential of dietary intervention in pregnant mothers to influence a protective effect in infants.
Past studies have linked apples, rich in antioxidants, with having an anti-cancer effect and Alzheimer's.
According to the European Federation of Allergy and Airway Diseases Patients Association (EFA), over 30m Europeans suffer from asthma, costing Europe €17.7bn every year.
The cost due to lost productivity is estimated to be around €9.8bn.
The condition is on the rise in the Western world and the most common long-term condition in the UK.
On the other hand, apple consumption in the UK has fallen from 207 g/person/day in 1974 to 173 g/person/day in 2004/5.
The researchers studied 1924 children born to women recruited during pregnancy and then followed up five years later.
The women were eating a diet which consisted of a variety of fruits and vegetables, including bananas, oranges and pears and broccoli, spinach and peas.
They found that: " No consistent associations were found between childhood outcomes and maternal intake of the analysed foods except for apples and fish.
Maternal apple intake was beneficially associated with wheeze, asthma and doctor confirmed asthma in the children.
Maternal fish consumption was beneficially associated with doctor-confirmed eczema. "
Associations have been made between maternal vitamin E, vitamin D and zinc intakes protecting against asthma, the researchers said, but few studies on the relationship between particular foods and asthma have been carried out.
They said: "The advantages of studying foods are that they contain a mixture of micronutrients that may contribute more than the sum of their parts, and that associations with micronutrients that may be currently unrecognised or not easily quantifiable can be examined.
"In addition, an evaluation of the associations with nutrients and foods will guide any future intervention study that could be the basis for a public health intervention to prevent asthma and atopic disease by dietary intervention."
However, the study found there was no link between apple intake and childhood eczema and hay fever.
The researchers found that instead "beneficial associations were found between maternal total fish intake and doctor confirmed eczema and currently treated eczema, and between maternal oily fish intake and doctor confirmed hay fever. "
They added that: " The specific association found with apples in this study suggests an effect specific to apples, possibly because of their phytochemical content such as flavonoids."
Source: Thorax Maternal food consumption during pregnancy and asthma, respiratory and atopic symptoms in 5-year-old children doi:10.1136/thx.2006.074187 Authors: S Willers, G Devereux, L Craig, G McNeill, A Wijga, W Abou El-Magd, S Turner, P Helms and A Seaton.